Pedro Sarabia's Libertad held a two-point buffer on Cerro Porteno heading into the 22nd and final round of the 2014 Clausura campaign.
And Libertad preserved that lead thanks to Rodrigo Lopez at the Estadio Manuel Ferreira on Saturday.
Lopez's goal two minutes into the second half gave Libertad the Apertura-Clausura double for the second time since the format was introduced in 2008.
Cerro were 2-0 winners at Sol de America also on Saturday.
Jose Ortigoza's second-half brace ensured Cerro finished runners-up ahead of Guarani, who routed hosts 3 de Febrero 4-0 on Friday.
Guarani had four different goalscorers, with Federico Santander, Jorge Mendoza, Fernando Fernandez and Luis de La Cruz all on target in the drubbing.
3 de Febrero (0.8864) were relegated to the Division Intermedia as a result of their three-year average points total.
Cellar-dwelling 12 de Octubre (0.7045) will join them in the second division after they were thrashed 4-1 by lowly Rubio Nu on Thursday.
Fourth-placed Sportivo Luqueno played out a goalless draw against Deportivo Capiata.
Meanwhile, General Diaz triumphed 3-1 over Olimpia via Jorge Gimenez's double.
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